Nootropic Design released a slick Arduino-based RGB matrix controller that attaches to the back of matrix and eliminates the need for a separate Arduino:

The RGB Matrix Backpack is a small board that connects to the back of the Adafruit 16×32 RGB LED Matrix Panel and is a very convenient way to control this awesome panel. The board is simply a small Arduino. You can easily program the board using the Arduino IDE. As you can see from the video, it’s possible to create great color animations, completely in Arduino programming!

To program the board, you’ll need a USB-Serial adapter or cable to connect to the board’s 6-pin serial connector. Or you can program the ATMega328 chip using your Arduino board and move the chip to the RGB Matrix Backpack for testing.